Interaction missing in results

[GBeattie]

Hey,

I've recently run the standard pipeline and we were surprised to see an interaction missing (Fasl - Fas) that we expected to see in the results.

I checked the object for the intermediate steps to see where this interaction may have been lost, I managed to find both genes in the var.features slot (so not omitted by identifyOverExpressedGenes), and in the LRsig slot (so not omitted by identifyOverExpressedInteractions), I also tried skipping the filterCommunication step. However the interaction is still not present when I run subsetCommunication(cc.clust, thresh = 2), I've also looked inside the "net" slots and can't see it.

Both genes are reasonably well expressed in a few hundred cells, what possible steps could be filtering this interaction out of the final results?

Thanks in advance for any assistance!

Gordon

[sqjin]

@GBeattie Can you trycellchat <- computeCommunProb(cellchat,type = "truncatedMean", trim = 0.1)? The default parameter compute the average expression per cell group using a very strict criteria.

[GBeattie]

Thanks for the suggestion, I've tried that, and I've tried setting trim = 0 just to check whether that helps, neither resulted in any more interactions coming through. To double check I put the data through CellPhoneDB and it does find several significant Fas/Fasl interactions between clusters. Would be great to know the reason as I definitely prefer CellChat's functionality!

[laijen000]

Hi @GBeattie , I am having a similar issue with some pathways of interest dropping out and I've been checking intermediate steps as well. Did you find a solution to this?

[sqjin]

@laijen000 Can you check the average expression of signaling genes of interest, e.g, computeAveExpr(cellchat, features = c("CXCL12","CXCR4"), type = "truncatedMean", trim = 0.1).